- PDB-3wo0: Crystal structure of Bacillus subtilis YwfE, an L-amino acid liga... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3wo0
Title
Crystal structure of Bacillus subtilis YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala
Components
Alanine-anticapsin ligase BacD
Keywords
LIGASE / ATP-grasp fold / ATP Binding
Function / homology
Function and homology information
L-alanine-L-anticapsin ligase / L-amino-acid alpha-ligase activity / antibiotic biosynthetic process / ATP binding / metal ion binding Similarity search - Function
Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2→20 Å / Num. obs: 40756 / % possible obs: 98.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 53.5
Reflection shell
Resolution: 2→2.02 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 8.3 / Num. unique all: 2654 / % possible all: 99.4
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Processing
Software
Name
Version
Classification
HKL-2000
datacollection
CRANK
phasing
REFMAC
5.7.0029
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2→19.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.806 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23593
2074
5.1 %
RANDOM
Rwork
0.19526
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obs
0.19736
38656
98.29 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK